rs4262642

Variant names:

• chr10-128047283-A-C
• rs4262642
• NM_006504.6:c.110-107A>C

Your query was ambiguous. Multiple possible variants found:

• chr10-128047283-A-C
• chr10-128047283-A-G
• chr10-128047283-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006504.6(PTPRE):​c.110-107A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.778 in 1,433,764 control chromosomes in the GnomAD database, including 434,401 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.78 (46086 hom., cov: 33)
  • Exomes 𝑓: 0.78 (388315 hom.)
• Consequence: PTPRE NM_006504.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.159
• Publications: 5 publications found

Genes affected

PTPRE (HGNC:9669): (protein tyrosine phosphatase receptor type E) The protein encoded by this gene is a member of the protein tyrosine phosphatase (PTP) family. PTPs are known to be signaling molecules that regulate a variety of cellular processes including cell growth, differentiation, mitotic cycle, and oncogenic transformation. Several alternatively spliced transcript variants of this gene have been reported, at least two of which encode a receptor-type PTP that possesses a short extracellular domain, a single transmembrane region, and two tandem intracytoplasmic catalytic domains; another one encodes a PTP that contains a distinct hydrophilic N-terminus, and thus represents a nonreceptor-type isoform of this PTP. Studies of the similar gene in mice suggested the regulatory roles of this PTP in RAS related signal transduction pathways, cytokine-induced SATA signaling, as well as the activation of voltage-gated K+ channels. [provided by RefSeq, Oct 2015]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.823 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTPRE	NM_006504.6	c.110-107A>C		intron_variant	Intron 3 of 20	ENST00000254667.8	NP_006495.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTPRE	ENST00000254667.8	c.110-107A>C		intron_variant	Intron 3 of 20	1	NM_006504.6	ENSP00000254667.3

Frequencies

GnomAD3 genomes AF: 0.777 AC: 118101 AN: 152034 Hom.: 46058 Cov.: 33

Gnomad AFR AF: 0.759

Gnomad AMI AF: 0.924

Gnomad AMR AF: 0.810

Gnomad ASJ AF: 0.735

Gnomad EAS AF: 0.844

Gnomad SAS AF: 0.771

Gnomad FIN AF: 0.730

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.784

Gnomad OTH AF: 0.756

GnomAD4 exome AF: 0.778 AC: 997135 AN: 1281612 Hom.: 388315 AF XY: 0.778 AC XY: 486639 AN XY: 625790

African (AFR) AF: 0.772 AC: 21955 AN: 28440

American (AMR) AF: 0.849 AC: 20589 AN: 24256

Ashkenazi Jewish (ASJ) AF: 0.735 AC: 14739 AN: 20044

East Asian (EAS) AF: 0.844 AC: 29505 AN: 34972

South Asian (SAS) AF: 0.767 AC: 51691 AN: 67378

European-Finnish (FIN) AF: 0.734 AC: 25554 AN: 34800

Middle Eastern (MID) AF: 0.760 AC: 3885 AN: 5110

European-Non Finnish (NFE) AF: 0.778 AC: 788077 AN: 1013294

Other (OTH) AF: 0.772 AC: 41140 AN: 53318

GnomAD4 genome AF: 0.777 AC: 118183 AN: 152152 Hom.: 46086 Cov.: 33 AF XY: 0.776 AC XY: 57726 AN XY: 74378

African (AFR) AF: 0.759 AC: 31511 AN: 41504

American (AMR) AF: 0.811 AC: 12394 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.735 AC: 2552 AN: 3470

East Asian (EAS) AF: 0.844 AC: 4359 AN: 5166

South Asian (SAS) AF: 0.770 AC: 3716 AN: 4828

European-Finnish (FIN) AF: 0.730 AC: 7724 AN: 10586

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.784 AC: 53274 AN: 67986

Other (OTH) AF: 0.750 AC: 1587 AN: 2116

Alfa AF: 0.780 Hom.: 196984

Bravo AF: 0.782

Asia WGS AF: 0.821 AC: 2855 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.9
DANN	Benign	0.63
PhyloP100		-0.16
PromoterAI		0.011	Neutral
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4262642; hg19: chr10-129845547;